{
  "nbformat": 4,
  "nbformat_minor": 0,
  "metadata": {
    "colab": {
      "name": "install.ipynb",
      "provenance": [],
      "authorship_tag": "ABX9TyNR6/pdZ2hVLiZq/dIfggeM",
      "include_colab_link": true
    },
    "kernelspec": {
      "name": "python3",
      "display_name": "Python 3"
    }
  },
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "view-in-github",
        "colab_type": "text"
      },
      "source": [
        "<a href=\"https://colab.research.google.com/github/tongzhugroup/reacnetgenerator/blob/master/tutorial/install.ipynb\" target=\"_parent\"><img src=\"https://img.njzjz.win/?url=colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "wRfG0B6jxcT0",
        "colab_type": "text"
      },
      "source": [
        "# Tutorial: Install ReacNetGenerator on Google Colaboratory \n",
        "\n",
        "In this series of tutorials, we will try to install and run ReacNetGenerator on [Google Colaboratory](https://colab.research.google.com/). You can click the above button to repeat it.\n",
        "\n",
        "In this tutorial, we will use `conda` to install ReacNetGenerator. This is the eastiest way without compiling the package.\n",
        "\n",
        "## Install Miniconda\n",
        "\n",
        "Firstly, we download the latest version of Miniconda 3 and then install it in `/usr/local`.\n"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "5sXRqqyTwJRa",
        "colab_type": "code",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 1000
        },
        "outputId": "8c2a5937-db59-4687-c754-0f9713a69169"
      },
      "source": [
        "%%bash\n",
        "MINICONDA_INSTALLER_SCRIPT=Miniconda3-latest-Linux-x86_64.sh\n",
        "MINICONDA_PREFIX=/usr/local\n",
        "wget https://repo.continuum.io/miniconda/$MINICONDA_INSTALLER_SCRIPT --no-verbose\n",
        "chmod +x $MINICONDA_INSTALLER_SCRIPT\n",
        "./$MINICONDA_INSTALLER_SCRIPT -b -f -p $MINICONDA_PREFIX"
      ],
      "execution_count": 1,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "PREFIX=/usr/local\n",
            "Unpacking payload ...\n",
            "Collecting package metadata (current_repodata.json): ...working... done\n",
            "Solving environment: ...working... done\n",
            "\n",
            "## Package Plan ##\n",
            "\n",
            "  environment location: /usr/local\n",
            "\n",
            "  added / updated specs:\n",
            "    - _libgcc_mutex==0.1=main\n",
            "    - ca-certificates==2020.1.1=0\n",
            "    - certifi==2020.4.5.1=py37_0\n",
            "    - cffi==1.14.0=py37he30daa8_1\n",
            "    - chardet==3.0.4=py37_1003\n",
            "    - conda-package-handling==1.6.1=py37h7b6447c_0\n",
            "    - conda==4.8.3=py37_0\n",
            "    - cryptography==2.9.2=py37h1ba5d50_0\n",
            "    - idna==2.9=py_1\n",
            "    - ld_impl_linux-64==2.33.1=h53a641e_7\n",
            "    - libedit==3.1.20181209=hc058e9b_0\n",
            "    - libffi==3.3=he6710b0_1\n",
            "    - libgcc-ng==9.1.0=hdf63c60_0\n",
            "    - libstdcxx-ng==9.1.0=hdf63c60_0\n",
            "    - ncurses==6.2=he6710b0_1\n",
            "    - openssl==1.1.1g=h7b6447c_0\n",
            "    - pip==20.0.2=py37_3\n",
            "    - pycosat==0.6.3=py37h7b6447c_0\n",
            "    - pycparser==2.20=py_0\n",
            "    - pyopenssl==19.1.0=py37_0\n",
            "    - pysocks==1.7.1=py37_0\n",
            "    - python==3.7.7=hcff3b4d_5\n",
            "    - readline==8.0=h7b6447c_0\n",
            "    - requests==2.23.0=py37_0\n",
            "    - ruamel_yaml==0.15.87=py37h7b6447c_0\n",
            "    - setuptools==46.4.0=py37_0\n",
            "    - six==1.14.0=py37_0\n",
            "    - sqlite==3.31.1=h62c20be_1\n",
            "    - tk==8.6.8=hbc83047_0\n",
            "    - tqdm==4.46.0=py_0\n",
            "    - urllib3==1.25.8=py37_0\n",
            "    - wheel==0.34.2=py37_0\n",
            "    - xz==5.2.5=h7b6447c_0\n",
            "    - yaml==0.1.7=had09818_2\n",
            "    - zlib==1.2.11=h7b6447c_3\n",
            "\n",
            "\n",
            "The following NEW packages will be INSTALLED:\n",
            "\n",
            "  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main\n",
            "  ca-certificates    pkgs/main/linux-64::ca-certificates-2020.1.1-0\n",
            "  certifi            pkgs/main/linux-64::certifi-2020.4.5.1-py37_0\n",
            "  cffi               pkgs/main/linux-64::cffi-1.14.0-py37he30daa8_1\n",
            "  chardet            pkgs/main/linux-64::chardet-3.0.4-py37_1003\n",
            "  conda              pkgs/main/linux-64::conda-4.8.3-py37_0\n",
            "  conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.6.1-py37h7b6447c_0\n",
            "  cryptography       pkgs/main/linux-64::cryptography-2.9.2-py37h1ba5d50_0\n",
            "  idna               pkgs/main/noarch::idna-2.9-py_1\n",
            "  ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.33.1-h53a641e_7\n",
            "  libedit            pkgs/main/linux-64::libedit-3.1.20181209-hc058e9b_0\n",
            "  libffi             pkgs/main/linux-64::libffi-3.3-he6710b0_1\n",
            "  libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0\n",
            "  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0\n",
            "  ncurses            pkgs/main/linux-64::ncurses-6.2-he6710b0_1\n",
            "  openssl            pkgs/main/linux-64::openssl-1.1.1g-h7b6447c_0\n",
            "  pip                pkgs/main/linux-64::pip-20.0.2-py37_3\n",
            "  pycosat            pkgs/main/linux-64::pycosat-0.6.3-py37h7b6447c_0\n",
            "  pycparser          pkgs/main/noarch::pycparser-2.20-py_0\n",
            "  pyopenssl          pkgs/main/linux-64::pyopenssl-19.1.0-py37_0\n",
            "  pysocks            pkgs/main/linux-64::pysocks-1.7.1-py37_0\n",
            "  python             pkgs/main/linux-64::python-3.7.7-hcff3b4d_5\n",
            "  readline           pkgs/main/linux-64::readline-8.0-h7b6447c_0\n",
            "  requests           pkgs/main/linux-64::requests-2.23.0-py37_0\n",
            "  ruamel_yaml        pkgs/main/linux-64::ruamel_yaml-0.15.87-py37h7b6447c_0\n",
            "  setuptools         pkgs/main/linux-64::setuptools-46.4.0-py37_0\n",
            "  six                pkgs/main/linux-64::six-1.14.0-py37_0\n",
            "  sqlite             pkgs/main/linux-64::sqlite-3.31.1-h62c20be_1\n",
            "  tk                 pkgs/main/linux-64::tk-8.6.8-hbc83047_0\n",
            "  tqdm               pkgs/main/noarch::tqdm-4.46.0-py_0\n",
            "  urllib3            pkgs/main/linux-64::urllib3-1.25.8-py37_0\n",
            "  wheel              pkgs/main/linux-64::wheel-0.34.2-py37_0\n",
            "  xz                 pkgs/main/linux-64::xz-5.2.5-h7b6447c_0\n",
            "  yaml               pkgs/main/linux-64::yaml-0.1.7-had09818_2\n",
            "  zlib               pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3\n",
            "\n",
            "\n",
            "Preparing transaction: ...working... done\n",
            "Executing transaction: ...working... done\n",
            "installation finished.\n",
            "WARNING:\n",
            "    You currently have a PYTHONPATH environment variable set. This may cause\n",
            "    unexpected behavior when running the Python interpreter in Miniconda3.\n",
            "    For best results, please verify that your PYTHONPATH only points to\n",
            "    directories of packages that are compatible with the Python interpreter\n",
            "    in Miniconda3: /usr/local\n"
          ],
          "name": "stdout"
        },
        {
          "output_type": "stream",
          "text": [
            "2020-06-28 21:24:34 URL:https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh [88867207/88867207] -> \"Miniconda3-latest-Linux-x86_64.sh\" [1]\n",
            "\r  0%|          | 0/35 [00:00<?, ?it/s]\rExtracting : conda-package-handling-1.6.1-py37h7b6447c_0.conda:   0%|          | 0/35 [00:00<?, ?it/s]\rExtracting : xz-5.2.5-h7b6447c_0.conda:   3%|▎         | 1/35 [00:00<00:02, 13.53it/s]                \rExtracting : readline-8.0-h7b6447c_0.conda:   6%|▌         | 2/35 [00:00<00:01, 17.12it/s]\rExtracting : readline-8.0-h7b6447c_0.conda:   9%|▊         | 3/35 [00:00<00:01, 25.65it/s]\rExtracting : openssl-1.1.1g-h7b6447c_0.conda:   9%|▊         | 3/35 [00:00<00:01, 25.65it/s]\rExtracting : openssl-1.1.1g-h7b6447c_0.conda:  11%|█▏        | 4/35 [00:00<00:01, 16.33it/s]\rExtracting : tk-8.6.8-hbc83047_0.conda:  11%|█▏        | 4/35 [00:00<00:01, 16.33it/s]      \rExtracting : pysocks-1.7.1-py37_0.conda:  14%|█▍        | 5/35 [00:00<00:01, 16.33it/s]\rExtracting : pysocks-1.7.1-py37_0.conda:  17%|█▋        | 6/35 [00:00<00:02, 12.27it/s]\rExtracting : pyopenssl-19.1.0-py37_0.conda:  17%|█▋        | 6/35 [00:00<00:02, 12.27it/s]\rExtracting : ruamel_yaml-0.15.87-py37h7b6447c_0.conda:  20%|██        | 7/35 [00:00<00:02, 12.27it/s]\rExtracting : urllib3-1.25.8-py37_0.conda:  23%|██▎       | 8/35 [00:00<00:02, 12.27it/s]             \rExtracting : sqlite-3.31.1-h62c20be_1.conda:  26%|██▌       | 9/35 [00:00<00:02, 12.27it/s]\rExtracting : python-3.7.7-hcff3b4d_5.conda:  29%|██▊       | 10/35 [00:01<00:02, 12.27it/s]\rExtracting : python-3.7.7-hcff3b4d_5.conda:  31%|███▏      | 11/35 [00:01<00:03,  7.55it/s]\rExtracting : zlib-1.2.11-h7b6447c_3.conda:  31%|███▏      | 11/35 [00:01<00:03,  7.55it/s] \rExtracting : cryptography-2.9.2-py37h1ba5d50_0.conda:  34%|███▍      | 12/35 [00:01<00:03,  7.55it/s]\rExtracting : tqdm-4.46.0-py_0.conda:  37%|███▋      | 13/35 [00:01<00:02,  7.55it/s]                 \rExtracting : certifi-2020.4.5.1-py37_0.conda:  40%|████      | 14/35 [00:01<00:02,  7.55it/s]\rExtracting : pip-20.0.2-py37_3.conda:  43%|████▎     | 15/35 [00:01<00:02,  7.55it/s]        \rExtracting : libedit-3.1.20181209-hc058e9b_0.conda:  46%|████▌     | 16/35 [00:01<00:02,  7.55it/s]\rExtracting : pycosat-0.6.3-py37h7b6447c_0.conda:  49%|████▊     | 17/35 [00:01<00:02,  7.55it/s]   \rExtracting : libgcc-ng-9.1.0-hdf63c60_0.conda:  51%|█████▏    | 18/35 [00:01<00:02,  7.55it/s]  \rExtracting : _libgcc_mutex-0.1-main.conda:  54%|█████▍    | 19/35 [00:01<00:02,  7.55it/s]    \rExtracting : ncurses-6.2-he6710b0_1.conda:  57%|█████▋    | 20/35 [00:01<00:01,  7.55it/s]\rExtracting : libffi-3.3-he6710b0_1.conda:  60%|██████    | 21/35 [00:01<00:01,  7.55it/s] \rExtracting : ca-certificates-2020.1.1-0.conda:  63%|██████▎   | 22/35 [00:01<00:01,  7.55it/s]\rExtracting : requests-2.23.0-py37_0.conda:  66%|██████▌   | 23/35 [00:01<00:01,  7.55it/s]    \rExtracting : chardet-3.0.4-py37_1003.conda:  69%|██████▊   | 24/35 [00:01<00:01,  7.55it/s]\rExtracting : ld_impl_linux-64-2.33.1-h53a641e_7.conda:  71%|███████▏  | 25/35 [00:01<00:01,  7.55it/s]\rExtracting : ld_impl_linux-64-2.33.1-h53a641e_7.conda:  74%|███████▍  | 26/35 [00:01<00:00, 10.50it/s]\rExtracting : pycparser-2.20-py_0.conda:  74%|███████▍  | 26/35 [00:01<00:00, 10.50it/s]               \rExtracting : six-1.14.0-py37_0.conda:  77%|███████▋  | 27/35 [00:01<00:00, 10.50it/s]  \rExtracting : wheel-0.34.2-py37_0.conda:  80%|████████  | 28/35 [00:01<00:00, 10.50it/s]\rExtracting : setuptools-46.4.0-py37_0.conda:  83%|████████▎ | 29/35 [00:01<00:00, 10.50it/s]\rExtracting : yaml-0.1.7-had09818_2.conda:  86%|████████▌ | 30/35 [00:01<00:00, 10.50it/s]   \rExtracting : yaml-0.1.7-had09818_2.conda:  89%|████████▊ | 31/35 [00:01<00:00, 13.48it/s]\rExtracting : idna-2.9-py_1.conda:  89%|████████▊ | 31/35 [00:01<00:00, 13.48it/s]        \rExtracting : cffi-1.14.0-py37he30daa8_1.conda:  91%|█████████▏| 32/35 [00:02<00:00, 13.48it/s]\rExtracting : libstdcxx-ng-9.1.0-hdf63c60_0.conda:  94%|█████████▍| 33/35 [00:02<00:00, 13.48it/s]\rExtracting : conda-4.8.3-py37_0.tar.bz2:  97%|█████████▋| 34/35 [00:02<00:00, 13.48it/s]         \r                                                                                        \r"
          ],
          "name": "stderr"
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "sfF2fuVHyu2M",
        "colab_type": "text"
      },
      "source": [
        "## Install ReacNetGenerator\n",
        "Then, we use `conda` to install the ReacNetGenerator from the [conda-forge](https://github.com/conda-forge) channel."
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "c5oBZFSQtKFi",
        "colab_type": "code",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 1000
        },
        "outputId": "58e4d4b3-06bf-4cfc-c7c6-14882e9fc429"
      },
      "source": [
        "!conda install reacnetgenerator -c conda-forge -y"
      ],
      "execution_count": 2,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "Collecting package metadata (current_repodata.json): - \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\bdone\n",
            "Solving environment: | \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\bdone\n",
            "\n",
            "## Package Plan ##\n",
            "\n",
            "  environment location: /usr/local\n",
            "\n",
            "  added / updated specs:\n",
            "    - reacnetgenerator\n",
            "\n",
            "\n",
            "The following packages will be downloaded:\n",
            "\n",
            "    package                    |            build\n",
            "    ---------------------------|-----------------\n",
            "    ase-3.19.1                 |             py_0         1.5 MB  conda-forge\n",
            "    boost-1.72.0               |   py37h9de70de_0         316 KB  conda-forge\n",
            "    boost-cpp-1.72.0           |       h8e57a91_0        21.8 MB  conda-forge\n",
            "    bzip2-1.0.8                |       h516909a_2         396 KB  conda-forge\n",
            "    ca-certificates-2020.6.20  |       hecda079_0         145 KB  conda-forge\n",
            "    cairo-1.16.0               |    hcf35c78_1003         1.5 MB  conda-forge\n",
            "    certifi-2020.6.20          |   py37hc8dfbb8_0         151 KB  conda-forge\n",
            "    click-7.1.2                |     pyh9f0ad1d_0          64 KB  conda-forge\n",
            "    coloredlogs-14.0           |   py37hc8dfbb8_1          59 KB  conda-forge\n",
            "    conda-4.8.3                |   py37hc8dfbb8_1         3.0 MB  conda-forge\n",
            "    cycler-0.10.0              |             py_2           9 KB  conda-forge\n",
            "    decorator-4.4.2            |             py_0          11 KB  conda-forge\n",
            "    flask-1.1.2                |     pyh9f0ad1d_0          70 KB  conda-forge\n",
            "    fontconfig-2.13.1          |    h86ecdb6_1001         340 KB  conda-forge\n",
            "    freetype-2.10.2            |       he06d7ca_0         905 KB  conda-forge\n",
            "    glib-2.65.0                |       h3eb4bd4_0         2.9 MB\n",
            "    hmmlearn-0.2.3             |   py37hc1659b7_1         148 KB  conda-forge\n",
            "    humanfriendly-8.2          |   py37hc8dfbb8_0         117 KB  conda-forge\n",
            "    icu-64.2                   |       he1b5a44_1        12.6 MB  conda-forge\n",
            "    itsdangerous-1.1.0         |             py_0          16 KB  conda-forge\n",
            "    jinja2-2.11.2              |     pyh9f0ad1d_0          93 KB  conda-forge\n",
            "    joblib-0.15.1              |             py_0         202 KB  conda-forge\n",
            "    jpeg-9d                    |       h516909a_0         266 KB  conda-forge\n",
            "    kiwisolver-1.2.0           |   py37h99015e2_0          87 KB  conda-forge\n",
            "    libblas-3.8.0              |      14_openblas          10 KB  conda-forge\n",
            "    libcblas-3.8.0             |      14_openblas          10 KB  conda-forge\n",
            "    libgfortran-ng-7.5.0       |       hdf63c60_6         1.7 MB  conda-forge\n",
            "    libiconv-1.15              |    h516909a_1006         2.0 MB  conda-forge\n",
            "    liblapack-3.8.0            |      14_openblas          10 KB  conda-forge\n",
            "    libopenblas-0.3.7          |       h5ec1e0e_6         7.6 MB  conda-forge\n",
            "    libpng-1.6.37              |       hed695b0_1         308 KB  conda-forge\n",
            "    libtiff-4.1.0              |       hc7e4089_6         668 KB  conda-forge\n",
            "    libuuid-2.32.1             |    h14c3975_1000          26 KB  conda-forge\n",
            "    libwebp-base-1.1.0         |       h516909a_3         845 KB  conda-forge\n",
            "    libxcb-1.13                |    h14c3975_1002         396 KB  conda-forge\n",
            "    libxml2-2.9.10             |       hee79883_0         1.3 MB  conda-forge\n",
            "    lz4-3.1.0                  |   py37h5a7ed16_0          44 KB  conda-forge\n",
            "    lz4-c-1.9.2                |       he1b5a44_1         226 KB  conda-forge\n",
            "    markupsafe-1.1.1           |   py37h8f50634_1          26 KB  conda-forge\n",
            "    matplotlib-base-3.2.2      |   py37h30547a4_0         7.1 MB  conda-forge\n",
            "    networkx-2.4               |             py_1         1.2 MB  conda-forge\n",
            "    numpy-1.18.5               |   py37h8960a57_0         5.1 MB  conda-forge\n",
            "    olefile-0.46               |             py_0          31 KB  conda-forge\n",
            "    openbabel-3.1.1            |   py37h200e996_0         5.5 MB  conda-forge\n",
            "    openssl-1.1.1g             |       h516909a_0         2.1 MB  conda-forge\n",
            "    pandas-1.0.5               |   py37h0da4684_0        10.1 MB  conda-forge\n",
            "    pcre-8.44                  |       he1b5a44_0         261 KB  conda-forge\n",
            "    pillow-7.1.2               |   py37h718be6c_0         658 KB  conda-forge\n",
            "    pixman-0.38.0              |    h516909a_1003         594 KB  conda-forge\n",
            "    pthread-stubs-0.4          |    h14c3975_1001           5 KB  conda-forge\n",
            "    pybase64-1.0.1             |   py37h8f50634_1          42 KB  conda-forge\n",
            "    pycairo-1.19.1             |   py37h01af8b0_3          77 KB  conda-forge\n",
            "    pyparsing-2.4.7            |     pyh9f0ad1d_0          60 KB  conda-forge\n",
            "    python-dateutil-2.8.1      |             py_0         220 KB  conda-forge\n",
            "    python_abi-3.7             |          1_cp37m           4 KB  conda-forge\n",
            "    pytz-2020.1                |     pyh9f0ad1d_0         227 KB  conda-forge\n",
            "    rdkit-2020.03.3            |   py37hdd87690_0        24.7 MB  conda-forge\n",
            "    reacnetgenerator-1.4.134   |   py37h99015e2_0         922 KB  conda-forge\n",
            "    scikit-learn-0.23.1        |   py37h8a51577_0         6.8 MB  conda-forge\n",
            "    scipy-1.5.0                |   py37ha3d9a3c_0        18.6 MB  conda-forge\n",
            "    scour-0.37                 |             py_0          45 KB  conda-forge\n",
            "    threadpoolctl-2.1.0        |     pyh5ca1d4c_0          15 KB  conda-forge\n",
            "    tk-8.6.10                  |       hed695b0_0         3.2 MB  conda-forge\n",
            "    tornado-6.0.4              |   py37h8f50634_1         639 KB  conda-forge\n",
            "    werkzeug-1.0.1             |     pyh9f0ad1d_0         239 KB  conda-forge\n",
            "    xorg-kbproto-1.0.7         |    h14c3975_1002          26 KB  conda-forge\n",
            "    xorg-libice-1.0.10         |       h516909a_0          57 KB  conda-forge\n",
            "    xorg-libsm-1.2.3           |    h84519dc_1000          25 KB  conda-forge\n",
            "    xorg-libx11-1.6.9          |       h516909a_0         918 KB  conda-forge\n",
            "    xorg-libxau-1.0.9          |       h14c3975_0          13 KB  conda-forge\n",
            "    xorg-libxdmcp-1.1.3        |       h516909a_0          18 KB  conda-forge\n",
            "    xorg-libxext-1.3.4         |       h516909a_0          51 KB  conda-forge\n",
            "    xorg-libxrender-0.9.10     |    h516909a_1002          31 KB  conda-forge\n",
            "    xorg-renderproto-0.11.1    |    h14c3975_1002           8 KB  conda-forge\n",
            "    xorg-xextproto-7.3.0       |    h14c3975_1002          27 KB  conda-forge\n",
            "    xorg-xproto-7.0.31         |    h14c3975_1007          72 KB  conda-forge\n",
            "    zstd-1.4.4                 |       h6597ccf_3         991 KB  conda-forge\n",
            "    ------------------------------------------------------------\n",
            "                                           Total:       152.4 MB\n",
            "\n",
            "The following NEW packages will be INSTALLED:\n",
            "\n",
            "  ase                conda-forge/noarch::ase-3.19.1-py_0\n",
            "  boost              conda-forge/linux-64::boost-1.72.0-py37h9de70de_0\n",
            "  boost-cpp          conda-forge/linux-64::boost-cpp-1.72.0-h8e57a91_0\n",
            "  bzip2              conda-forge/linux-64::bzip2-1.0.8-h516909a_2\n",
            "  cairo              conda-forge/linux-64::cairo-1.16.0-hcf35c78_1003\n",
            "  click              conda-forge/noarch::click-7.1.2-pyh9f0ad1d_0\n",
            "  coloredlogs        conda-forge/linux-64::coloredlogs-14.0-py37hc8dfbb8_1\n",
            "  cycler             conda-forge/noarch::cycler-0.10.0-py_2\n",
            "  decorator          conda-forge/noarch::decorator-4.4.2-py_0\n",
            "  flask              conda-forge/noarch::flask-1.1.2-pyh9f0ad1d_0\n",
            "  fontconfig         conda-forge/linux-64::fontconfig-2.13.1-h86ecdb6_1001\n",
            "  freetype           conda-forge/linux-64::freetype-2.10.2-he06d7ca_0\n",
            "  glib               pkgs/main/linux-64::glib-2.65.0-h3eb4bd4_0\n",
            "  hmmlearn           conda-forge/linux-64::hmmlearn-0.2.3-py37hc1659b7_1\n",
            "  humanfriendly      conda-forge/linux-64::humanfriendly-8.2-py37hc8dfbb8_0\n",
            "  icu                conda-forge/linux-64::icu-64.2-he1b5a44_1\n",
            "  itsdangerous       conda-forge/noarch::itsdangerous-1.1.0-py_0\n",
            "  jinja2             conda-forge/noarch::jinja2-2.11.2-pyh9f0ad1d_0\n",
            "  joblib             conda-forge/noarch::joblib-0.15.1-py_0\n",
            "  jpeg               conda-forge/linux-64::jpeg-9d-h516909a_0\n",
            "  kiwisolver         conda-forge/linux-64::kiwisolver-1.2.0-py37h99015e2_0\n",
            "  libblas            conda-forge/linux-64::libblas-3.8.0-14_openblas\n",
            "  libcblas           conda-forge/linux-64::libcblas-3.8.0-14_openblas\n",
            "  libgfortran-ng     conda-forge/linux-64::libgfortran-ng-7.5.0-hdf63c60_6\n",
            "  libiconv           conda-forge/linux-64::libiconv-1.15-h516909a_1006\n",
            "  liblapack          conda-forge/linux-64::liblapack-3.8.0-14_openblas\n",
            "  libopenblas        conda-forge/linux-64::libopenblas-0.3.7-h5ec1e0e_6\n",
            "  libpng             conda-forge/linux-64::libpng-1.6.37-hed695b0_1\n",
            "  libtiff            conda-forge/linux-64::libtiff-4.1.0-hc7e4089_6\n",
            "  libuuid            conda-forge/linux-64::libuuid-2.32.1-h14c3975_1000\n",
            "  libwebp-base       conda-forge/linux-64::libwebp-base-1.1.0-h516909a_3\n",
            "  libxcb             conda-forge/linux-64::libxcb-1.13-h14c3975_1002\n",
            "  libxml2            conda-forge/linux-64::libxml2-2.9.10-hee79883_0\n",
            "  lz4                conda-forge/linux-64::lz4-3.1.0-py37h5a7ed16_0\n",
            "  lz4-c              conda-forge/linux-64::lz4-c-1.9.2-he1b5a44_1\n",
            "  markupsafe         conda-forge/linux-64::markupsafe-1.1.1-py37h8f50634_1\n",
            "  matplotlib-base    conda-forge/linux-64::matplotlib-base-3.2.2-py37h30547a4_0\n",
            "  networkx           conda-forge/noarch::networkx-2.4-py_1\n",
            "  numpy              conda-forge/linux-64::numpy-1.18.5-py37h8960a57_0\n",
            "  olefile            conda-forge/noarch::olefile-0.46-py_0\n",
            "  openbabel          conda-forge/linux-64::openbabel-3.1.1-py37h200e996_0\n",
            "  pandas             conda-forge/linux-64::pandas-1.0.5-py37h0da4684_0\n",
            "  pcre               conda-forge/linux-64::pcre-8.44-he1b5a44_0\n",
            "  pillow             conda-forge/linux-64::pillow-7.1.2-py37h718be6c_0\n",
            "  pixman             conda-forge/linux-64::pixman-0.38.0-h516909a_1003\n",
            "  pthread-stubs      conda-forge/linux-64::pthread-stubs-0.4-h14c3975_1001\n",
            "  pybase64           conda-forge/linux-64::pybase64-1.0.1-py37h8f50634_1\n",
            "  pycairo            conda-forge/linux-64::pycairo-1.19.1-py37h01af8b0_3\n",
            "  pyparsing          conda-forge/noarch::pyparsing-2.4.7-pyh9f0ad1d_0\n",
            "  python-dateutil    conda-forge/noarch::python-dateutil-2.8.1-py_0\n",
            "  python_abi         conda-forge/linux-64::python_abi-3.7-1_cp37m\n",
            "  pytz               conda-forge/noarch::pytz-2020.1-pyh9f0ad1d_0\n",
            "  rdkit              conda-forge/linux-64::rdkit-2020.03.3-py37hdd87690_0\n",
            "  reacnetgenerator   conda-forge/linux-64::reacnetgenerator-1.4.134-py37h99015e2_0\n",
            "  scikit-learn       conda-forge/linux-64::scikit-learn-0.23.1-py37h8a51577_0\n",
            "  scipy              conda-forge/linux-64::scipy-1.5.0-py37ha3d9a3c_0\n",
            "  scour              conda-forge/noarch::scour-0.37-py_0\n",
            "  threadpoolctl      conda-forge/noarch::threadpoolctl-2.1.0-pyh5ca1d4c_0\n",
            "  tornado            conda-forge/linux-64::tornado-6.0.4-py37h8f50634_1\n",
            "  werkzeug           conda-forge/noarch::werkzeug-1.0.1-pyh9f0ad1d_0\n",
            "  xorg-kbproto       conda-forge/linux-64::xorg-kbproto-1.0.7-h14c3975_1002\n",
            "  xorg-libice        conda-forge/linux-64::xorg-libice-1.0.10-h516909a_0\n",
            "  xorg-libsm         conda-forge/linux-64::xorg-libsm-1.2.3-h84519dc_1000\n",
            "  xorg-libx11        conda-forge/linux-64::xorg-libx11-1.6.9-h516909a_0\n",
            "  xorg-libxau        conda-forge/linux-64::xorg-libxau-1.0.9-h14c3975_0\n",
            "  xorg-libxdmcp      conda-forge/linux-64::xorg-libxdmcp-1.1.3-h516909a_0\n",
            "  xorg-libxext       conda-forge/linux-64::xorg-libxext-1.3.4-h516909a_0\n",
            "  xorg-libxrender    conda-forge/linux-64::xorg-libxrender-0.9.10-h516909a_1002\n",
            "  xorg-renderproto   conda-forge/linux-64::xorg-renderproto-0.11.1-h14c3975_1002\n",
            "  xorg-xextproto     conda-forge/linux-64::xorg-xextproto-7.3.0-h14c3975_1002\n",
            "  xorg-xproto        conda-forge/linux-64::xorg-xproto-7.0.31-h14c3975_1007\n",
            "  zstd               conda-forge/linux-64::zstd-1.4.4-h6597ccf_3\n",
            "\n",
            "The following packages will be UPDATED:\n",
            "\n",
            "  ca-certificates     pkgs/main::ca-certificates-2020.1.1-0 --> conda-forge::ca-certificates-2020.6.20-hecda079_0\n",
            "  certifi              pkgs/main::certifi-2020.4.5.1-py37_0 --> conda-forge::certifi-2020.6.20-py37hc8dfbb8_0\n",
            "  conda                       pkgs/main::conda-4.8.3-py37_0 --> conda-forge::conda-4.8.3-py37hc8dfbb8_1\n",
            "  tk                         pkgs/main::tk-8.6.8-hbc83047_0 --> conda-forge::tk-8.6.10-hed695b0_0\n",
            "\n",
            "The following packages will be SUPERSEDED by a higher-priority channel:\n",
            "\n",
            "  openssl              pkgs/main::openssl-1.1.1g-h7b6447c_0 --> conda-forge::openssl-1.1.1g-h516909a_0\n",
            "\n",
            "\n",
            "\n",
            "Downloading and Extracting Packages\n",
            "olefile-0.46         | 31 KB     | : 100% 1.0/1 [00:00<00:00,  9.55it/s]\n",
            "kiwisolver-1.2.0     | 87 KB     | : 100% 1.0/1 [00:00<00:00, 13.47it/s]\n",
            "jinja2-2.11.2        | 93 KB     | : 100% 1.0/1 [00:00<00:00, 16.98it/s]\n",
            "xorg-libxrender-0.9. | 31 KB     | : 100% 1.0/1 [00:00<00:00, 25.09it/s]\n",
            "click-7.1.2          | 64 KB     | : 100% 1.0/1 [00:00<00:00, 19.64it/s]\n",
            "libxcb-1.13          | 396 KB    | : 100% 1.0/1 [00:00<00:00,  6.33it/s]\n",
            "libcblas-3.8.0       | 10 KB     | : 100% 1.0/1 [00:00<00:00, 26.01it/s]\n",
            "conda-4.8.3          | 3.0 MB    | : 100% 1.0/1 [00:00<00:00,  1.41it/s]\n",
            "markupsafe-1.1.1     | 26 KB     | : 100% 1.0/1 [00:00<00:00, 23.41it/s]\n",
            "xorg-xproto-7.0.31   | 72 KB     | : 100% 1.0/1 [00:00<00:00, 17.66it/s]\n",
            "freetype-2.10.2      | 905 KB    | : 100% 1.0/1 [00:00<00:00,  4.41it/s]\n",
            "tornado-6.0.4        | 639 KB    | : 100% 1.0/1 [00:00<00:00,  4.73it/s]\n",
            "fontconfig-2.13.1    | 340 KB    | : 100% 1.0/1 [00:00<00:00,  9.28it/s]\n",
            "rdkit-2020.03.3      | 24.7 MB   | : 100% 1.0/1 [00:04<00:00,  4.38s/it]               \n",
            "xorg-libxau-1.0.9    | 13 KB     | : 100% 1.0/1 [00:00<00:00, 21.93it/s]\n",
            "decorator-4.4.2      | 11 KB     | : 100% 1.0/1 [00:00<00:00, 23.99it/s]\n",
            "liblapack-3.8.0      | 10 KB     | : 100% 1.0/1 [00:00<00:00, 20.11it/s]\n",
            "libopenblas-0.3.7    | 7.6 MB    | : 100% 1.0/1 [00:01<00:00,  1.64s/it]\n",
            "bzip2-1.0.8          | 396 KB    | : 100% 1.0/1 [00:00<00:00,  8.82it/s]\n",
            "scikit-learn-0.23.1  | 6.8 MB    | : 100% 1.0/1 [00:01<00:00,  1.72s/it]\n",
            "pthread-stubs-0.4    | 5 KB      | : 100% 1.0/1 [00:00<00:00, 19.70it/s]\n",
            "boost-cpp-1.72.0     | 21.8 MB   | : 100% 1.0/1 [00:08<00:00,  8.42s/it]              \n",
            "libpng-1.6.37        | 308 KB    | : 100% 1.0/1 [00:00<00:00,  9.53it/s]\n",
            "libxml2-2.9.10       | 1.3 MB    | : 100% 1.0/1 [00:00<00:00,  2.14it/s]\n",
            "glib-2.65.0          | 2.9 MB    | : 100% 1.0/1 [00:00<00:00,  1.75s/it]                \n",
            "werkzeug-1.0.1       | 239 KB    | : 100% 1.0/1 [00:00<00:00,  9.93it/s]\n",
            "libiconv-1.15        | 2.0 MB    | : 100% 1.0/1 [00:00<00:00,  3.25it/s]\n",
            "scipy-1.5.0          | 18.6 MB   | : 100% 1.0/1 [00:03<00:00,  3.65s/it]               \n",
            "numpy-1.18.5         | 5.1 MB    | : 100% 1.0/1 [00:01<00:00,  1.17s/it]\n",
            "humanfriendly-8.2    | 117 KB    | : 100% 1.0/1 [00:00<00:00, 12.21it/s]\n",
            "matplotlib-base-3.2. | 7.1 MB    | : 100% 1.0/1 [00:01<00:00,  1.49s/it]\n",
            "pytz-2020.1          | 227 KB    | : 100% 1.0/1 [00:00<00:00,  3.47it/s]\n",
            "certifi-2020.6.20    | 151 KB    | : 100% 1.0/1 [00:00<00:00, 17.72it/s]\n",
            "flask-1.1.2          | 70 KB     | : 100% 1.0/1 [00:00<00:00, 18.93it/s]\n",
            "libwebp-base-1.1.0   | 845 KB    | : 100% 1.0/1 [00:00<00:00,  5.16it/s]\n",
            "coloredlogs-14.0     | 59 KB     | : 100% 1.0/1 [00:00<00:00, 22.23it/s]\n",
            "threadpoolctl-2.1.0  | 15 KB     | : 100% 1.0/1 [00:00<00:00, 29.89it/s]\n",
            "joblib-0.15.1        | 202 KB    | : 100% 1.0/1 [00:00<00:00, 11.62it/s]\n",
            "cycler-0.10.0        | 9 KB      | : 100% 1.0/1 [00:00<00:00, 29.45it/s]\n",
            "python-dateutil-2.8. | 220 KB    | : 100% 1.0/1 [00:00<00:00, 16.99it/s]\n",
            "pyparsing-2.4.7      | 60 KB     | : 100% 1.0/1 [00:00<00:00, 21.54it/s]\n",
            "pixman-0.38.0        | 594 KB    | : 100% 1.0/1 [00:00<00:00,  7.01it/s]\n",
            "libtiff-4.1.0        | 668 KB    | : 100% 1.0/1 [00:00<00:00,  5.99it/s]\n",
            "boost-1.72.0         | 316 KB    | : 100% 1.0/1 [00:00<00:00,  6.84it/s]\n",
            "ase-3.19.1           | 1.5 MB    | : 100% 1.0/1 [00:00<00:00,  1.98it/s]\n",
            "xorg-libxext-1.3.4   | 51 KB     | : 100% 1.0/1 [00:00<00:00, 22.65it/s]\n",
            "xorg-renderproto-0.1 | 8 KB      | : 100% 1.0/1 [00:00<00:00, 27.85it/s]\n",
            "itsdangerous-1.1.0   | 16 KB     | : 100% 1.0/1 [00:00<00:00, 25.90it/s]\n",
            "hmmlearn-0.2.3       | 148 KB    | : 100% 1.0/1 [00:00<00:00, 16.45it/s]\n",
            "zstd-1.4.4           | 991 KB    | : 100% 1.0/1 [00:00<00:00,  4.90it/s]\n",
            "pycairo-1.19.1       | 77 KB     | : 100% 1.0/1 [00:00<00:00, 22.89it/s]\n",
            "cairo-1.16.0         | 1.5 MB    | : 100% 1.0/1 [00:00<00:00,  2.80it/s]\n",
            "xorg-libxdmcp-1.1.3  | 18 KB     | : 100% 1.0/1 [00:00<00:00, 29.29it/s]\n",
            "networkx-2.4         | 1.2 MB    | : 100% 1.0/1 [00:00<00:00,  2.96it/s]\n",
            "xorg-libsm-1.2.3     | 25 KB     | : 100% 1.0/1 [00:00<00:00, 27.53it/s]\n",
            "libuuid-2.32.1       | 26 KB     | : 100% 1.0/1 [00:00<00:00, 22.59it/s]\n",
            "openbabel-3.1.1      | 5.5 MB    | : 100% 1.0/1 [00:01<00:00,  1.24s/it]\n",
            "tk-8.6.10            | 3.2 MB    | : 100% 1.0/1 [00:00<00:00,  1.48it/s]\n",
            "python_abi-3.7       | 4 KB      | : 100% 1.0/1 [00:00<00:00, 26.24it/s]\n",
            "pcre-8.44            | 261 KB    | : 100% 1.0/1 [00:00<00:00, 10.38it/s]\n",
            "libgfortran-ng-7.5.0 | 1.7 MB    | : 100% 1.0/1 [00:00<00:00,  2.81it/s]\n",
            "jpeg-9d              | 266 KB    | : 100% 1.0/1 [00:00<00:00, 10.85it/s]\n",
            "icu-64.2             | 12.6 MB   | : 100% 1.0/1 [00:02<00:00,  1.67s/it]               \n",
            "xorg-kbproto-1.0.7   | 26 KB     | : 100% 1.0/1 [00:00<00:00, 23.13it/s]\n",
            "xorg-libice-1.0.10   | 57 KB     | : 100% 1.0/1 [00:00<00:00, 22.86it/s]\n",
            "libblas-3.8.0        | 10 KB     | : 100% 1.0/1 [00:00<00:00, 23.85it/s]\n",
            "scour-0.37           | 45 KB     | : 100% 1.0/1 [00:00<00:00, 24.35it/s]\n",
            "openssl-1.1.1g       | 2.1 MB    | : 100% 1.0/1 [00:00<00:00,  2.58it/s]\n",
            "lz4-c-1.9.2          | 226 KB    | : 100% 1.0/1 [00:00<00:00, 11.83it/s]\n",
            "xorg-libx11-1.6.9    | 918 KB    | : 100% 1.0/1 [00:00<00:00,  4.99it/s]\n",
            "pillow-7.1.2         | 658 KB    | : 100% 1.0/1 [00:00<00:00,  5.44it/s]\n",
            "xorg-xextproto-7.3.0 | 27 KB     | : 100% 1.0/1 [00:00<00:00, 24.72it/s]\n",
            "ca-certificates-2020 | 145 KB    | : 100% 1.0/1 [00:00<00:00, 19.78it/s]\n",
            "lz4-3.1.0            | 44 KB     | : 100% 1.0/1 [00:00<00:00, 21.69it/s]\n",
            "pybase64-1.0.1       | 42 KB     | : 100% 1.0/1 [00:00<00:00, 18.07it/s]\n",
            "reacnetgenerator-1.4 | 922 KB    | : 100% 1.0/1 [00:00<00:00,  4.49it/s]\n",
            "pandas-1.0.5         | 10.1 MB   | : 100% 1.0/1 [00:02<00:00,  1.23s/it]               \n",
            "Preparing transaction: \\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\bdone\n",
            "Verifying transaction: / \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\bdone\n",
            "Executing transaction: \\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\bdone\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "Z-8L5vVKy9tc",
        "colab_type": "text"
      },
      "source": [
        "Now, ReacNetGenerator has been already installed in the environment. Try it now!"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "ceO8qwJtxGxo",
        "colab_type": "code",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 682
        },
        "outputId": "4c0f1534-bdb6-41e9-f39e-0cdbf368bd82"
      },
      "source": [
        "!reacnetgenerator -h"
      ],
      "execution_count": 3,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "usage: reacnetgenerator [-h] -i [INPUTFILENAME [INPUTFILENAME ...]] -a\n",
            "                        [ATOMNAME [ATOMNAME ...]] [--nohmm] [--dump]\n",
            "                        [--type TYPE] [--nopbc] [--cell CELL CELL CELL]\n",
            "                        [-n NPROC] [-s [SELECTATOMS [SELECTATOMS ...]]]\n",
            "                        [--stepinterval STEPINTERVAL] [--split SPLIT]\n",
            "                        [--maxspecies MAXSPECIES]\n",
            "                        [--matrixa MATRIXA MATRIXA MATRIXA MATRIXA]\n",
            "                        [--matrixb MATRIXB MATRIXB MATRIXB MATRIXB]\n",
            "                        [--urls URLS URLS]\n",
            "\n",
            "ReacNetGenerator 1.0.0\n",
            "\n",
            "optional arguments:\n",
            "  -h, --help            show this help message and exit\n",
            "  -i [INPUTFILENAME [INPUTFILENAME ...]], --inputfilename [INPUTFILENAME [INPUTFILENAME ...]]\n",
            "                        Input trajectory file, e.g. bonds.reaxc\n",
            "  -a [ATOMNAME [ATOMNAME ...]], --atomname [ATOMNAME [ATOMNAME ...]]\n",
            "                        Atomic names in the trajectory, e.g. C H O\n",
            "  --nohmm               Process trajectory without Hidden Markov Model (HMM)\n",
            "  --dump                Process the LAMMPS dump file\n",
            "  --type TYPE, -t TYPE  Input file type\n",
            "  --nopbc               Disable PBC.\n",
            "  --cell CELL CELL CELL, -c CELL CELL CELL\n",
            "                        Cell\n",
            "  -n NPROC, -np NPROC, --nproc NPROC\n",
            "                        Number of processes\n",
            "  -s [SELECTATOMS [SELECTATOMS ...]], --selectatoms [SELECTATOMS [SELECTATOMS ...]]\n",
            "                        Select atoms in the reaction network, e.g. C\n",
            "  --stepinterval STEPINTERVAL\n",
            "                        Step interval\n",
            "  --split SPLIT         Split number for the time axis\n",
            "  --maxspecies MAXSPECIES\n",
            "                        Max number of nodes (species) in the network\n",
            "  --matrixa MATRIXA MATRIXA MATRIXA MATRIXA\n",
            "                        Matrix A of HMM parameters\n",
            "  --matrixb MATRIXB MATRIXB MATRIXB MATRIXB\n",
            "                        Matrix B of HMM parameters\n",
            "  --urls URLS URLS      Download files\n"
          ],
          "name": "stdout"
        }
      ]
    }
  ]
}
